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Conserved domains on  [gi|155030242|ref|NP_060521|]
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cytoplasmic dynein 2 intermediate chain 1 isoform a [Homo sapiens]

Protein Classification

WD40 repeat domain-containing protein( domain architecture ID 11455410)

WD40 repeat domain-containing protein similar to proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly

CATH:  2.130.10.10
PubMed:  10322433|8090199
SCOP:  4002744

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00121 super family cl31754
MAEBL; Provisional
 5-453 1.46e-08

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 59.38  E-value: 1.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    5 KRRTKDDTWKADDLRKHLWAIQSGGSKEERKHREKKLRKESEM----DLPEHKEPRCRDPDQDARSRDRVAE--VHTAKE 78
Cdd:PTZ00121 1247 EERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKkkadEAKKAEEKKKADEAKKKAEEAKKADeaKKKAEE 1326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   79 SPRGERDRDRQRERRRDAKDREKEKLKEKHREAEKSHSRGKDREKEKDRRARKEELRQTVAHHNLLGQETRDRQllERAE 158
Cdd:PTZ00121 1327 AKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKA--EEDK 1404

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  159 RKGRSVSKVRSEEKDEDSERGDEDRERRYRERKLQYGDSKDnplkywlyKEEGERRHRKPREPDRDNKHREKSSTREKRE 238
Cdd:PTZ00121 1405 KKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKK--------ADEAKKKAEEAKKAEEAKKKAEEAKKADEAK 1476

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  239 KYSKEKSNSFSDKGEERHKEKRHKEGFHFDDERHQSNVDRK--EKSAKDEPRKRESQNGEHRNRGASSKRDGTSSQHAEN 316
Cdd:PTZ00121 1477 KKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKaeEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEE 1556

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  317 LVRNHGKDKDSRRKHGHEEGSSVWWKLDQRPGGEETVEIEKEETDLENARADAYTASCEDDFEDYEddfevcdgddDESS 396
Cdd:PTZ00121 1557 LKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKA----------EELK 1626

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  397 NEPESREKLEELPLAQKKEIQEIQRAINAENE---RIGELSLKLFQKRGRTEFEKEPRTD 453
Cdd:PTZ00121 1627 KAEEEKKKVEQLKKKEAEEKKKAEELKKAEEEnkiKAAEEAKKAEEDKKKAEEAKKAEED 1686
WD40 super family cl29593
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 912-984 1.21e-03

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


The actual alignment was detected with superfamily member cd00200:

Pssm-ID: 475233 [Multi-domain]  Cd Length: 289  Bit Score: 41.94  E-value: 1.21e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 155030242  912 VNVIDFSPFGEPiFLAGCSDGSIRLHQLSSAFPLLQWDSSTDshAVTGLQWSPTRpAVFLVQDDTSNIYIWDL 984
Cdd:cd00200   180 VNSVAFSPDGEK-LLSSSSDGTIKLWDLSTGKCLGTLRGHEN--GVNSVAFSPDG-YLLASGSEDGTIRVWDL 248
 
Name Accession Description Interval E-value
PTZ00121 PTZ00121
MAEBL; Provisional
 5-453 1.46e-08

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 59.38  E-value: 1.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    5 KRRTKDDTWKADDLRKHLWAIQSGGSKEERKHREKKLRKESEM----DLPEHKEPRCRDPDQDARSRDRVAE--VHTAKE 78
Cdd:PTZ00121 1247 EERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKkkadEAKKAEEKKKADEAKKKAEEAKKADeaKKKAEE 1326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   79 SPRGERDRDRQRERRRDAKDREKEKLKEKHREAEKSHSRGKDREKEKDRRARKEELRQTVAHHNLLGQETRDRQllERAE 158
Cdd:PTZ00121 1327 AKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKA--EEDK 1404

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  159 RKGRSVSKVRSEEKDEDSERGDEDRERRYRERKLQYGDSKDnplkywlyKEEGERRHRKPREPDRDNKHREKSSTREKRE 238
Cdd:PTZ00121 1405 KKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKK--------ADEAKKKAEEAKKAEEAKKKAEEAKKADEAK 1476

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  239 KYSKEKSNSFSDKGEERHKEKRHKEGFHFDDERHQSNVDRK--EKSAKDEPRKRESQNGEHRNRGASSKRDGTSSQHAEN 316
Cdd:PTZ00121 1477 KKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKaeEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEE 1556

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  317 LVRNHGKDKDSRRKHGHEEGSSVWWKLDQRPGGEETVEIEKEETDLENARADAYTASCEDDFEDYEddfevcdgddDESS 396
Cdd:PTZ00121 1557 LKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKA----------EELK 1626

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  397 NEPESREKLEELPLAQKKEIQEIQRAINAENE---RIGELSLKLFQKRGRTEFEKEPRTD 453
Cdd:PTZ00121 1627 KAEEEKKKVEQLKKKEAEEKKKAEELKKAEEEnkiKAAEEAKKAEEDKKKAEEAKKAEED 1686
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 18-300 4.84e-06

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 50.89  E-value: 4.84e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    18 LRKHLWAIQSGGSKEERKHREKKLRKESEMdLPEHKEPRCRDPDQdarsRDRVAEVHTAKESprgerdrdrqRERRRDAK 97
Cdd:pfam17380  271 LNQLLHIVQHQKAVSERQQQEKFEKMEQER-LRQEKEEKAREVER----RRKLEEAEKARQA----------EMDRQAAI 335

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    98 DREKEKLK-EKHREAEKSHSRGKDREKEkdrRARKEELRQTVAHHNLLGQETRDRQLL-ERAERKGRSVSKVRSEEkdED 175
Cdd:pfam17380  336 YAEQERMAmERERELERIRQEERKRELE---RIRQEEIAMEISRMRELERLQMERQQKnERVRQELEAARKVKILE--EE 410

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   176 SERGDEDRERRYRERKLQYGDSKDNPLKYW----------LYKEEGERRHRKPR----EPDRDNKHREKSSTREKREKYS 241
Cdd:pfam17380  411 RQRKIQQQKVEMEQIRAEQEEARQREVRRLeeeraremerVRLEEQERQQQVERlrqqEEERKRKKLELEKEKRDRKRAE 490

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 155030242   242 KEKSNSFSDKGEERHK----EKRHKEGFHFDDERHQSNVDRKEKSAKDEPRKRESQNGEHRNR 300
Cdd:pfam17380  491 EQRRKILEKELEERKQamieEERKRKLLEKEMEERQKAIYEEERRREAEEERRKQQEMEERRR 553
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 97-248 9.11e-05

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 46.42  E-value: 9.11e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    97 KDREKEKLKEKHREaekshsRGKDREKEKDRRARKEELRQTVAHHnllgqETRDRQLLERAERKGRSVSKVRSEEKDEDS 176
Cdd:TIGR01642    1 RDEEPDREREKSRG------RDRDRSSERPRRRSRDRSRFRDRHR-----RSRERSYREDSRPRDRRRYDSRSPRSLRYS 69

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 155030242   177 ERGDedrerryrerklqygdSKDNPlkywlykeegeRRHRKPREPDRDNKHREKSSTREKREKYSKEKSNSF 248
Cdd:TIGR01642   70 SVRR----------------SRDRP-----------RRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLW 114
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 912-984 1.21e-03

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 41.94  E-value: 1.21e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 155030242  912 VNVIDFSPFGEPiFLAGCSDGSIRLHQLSSAFPLLQWDSSTDshAVTGLQWSPTRpAVFLVQDDTSNIYIWDL 984
Cdd:cd00200   180 VNSVAFSPDGEK-LLSSSSDGTIKLWDLSTGKCLGTLRGHEN--GVNSVAFSPDG-YLLASGSEDGTIRVWDL 248
 
Name Accession Description Interval E-value
PTZ00121 PTZ00121
MAEBL; Provisional
 5-453 1.46e-08

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 59.38  E-value: 1.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    5 KRRTKDDTWKADDLRKHLWAIQSGGSKEERKHREKKLRKESEM----DLPEHKEPRCRDPDQDARSRDRVAE--VHTAKE 78
Cdd:PTZ00121 1247 EERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKkkadEAKKAEEKKKADEAKKKAEEAKKADeaKKKAEE 1326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   79 SPRGERDRDRQRERRRDAKDREKEKLKEKHREAEKSHSRGKDREKEKDRRARKEELRQTVAHHNLLGQETRDRQllERAE 158
Cdd:PTZ00121 1327 AKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKA--EEDK 1404

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  159 RKGRSVSKVRSEEKDEDSERGDEDRERRYRERKLQYGDSKDnplkywlyKEEGERRHRKPREPDRDNKHREKSSTREKRE 238
Cdd:PTZ00121 1405 KKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKK--------ADEAKKKAEEAKKAEEAKKKAEEAKKADEAK 1476

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  239 KYSKEKSNSFSDKGEERHKEKRHKEGFHFDDERHQSNVDRK--EKSAKDEPRKRESQNGEHRNRGASSKRDGTSSQHAEN 316
Cdd:PTZ00121 1477 KKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKaeEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEE 1556

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  317 LVRNHGKDKDSRRKHGHEEGSSVWWKLDQRPGGEETVEIEKEETDLENARADAYTASCEDDFEDYEddfevcdgddDESS 396
Cdd:PTZ00121 1557 LKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKA----------EELK 1626

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  397 NEPESREKLEELPLAQKKEIQEIQRAINAENE---RIGELSLKLFQKRGRTEFEKEPRTD 453
Cdd:PTZ00121 1627 KAEEEKKKVEQLKKKEAEEKKKAEELKKAEEEnkiKAAEEAKKAEEDKKKAEEAKKAEED 1686
PTZ00121 PTZ00121
MAEBL; Provisional
 2-325 4.72e-08

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 57.46  E-value: 4.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    2 EPGKRRTKDDTWKADDLRKhlwAIQSGGSKEERKHREKKLRKESEMDLPEHKEPRCRDPDQDARSRDRVAEVHTAKESPR 81
Cdd:PTZ00121 1394 DEAKKKAEEDKKKADELKK---AAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAK 1470

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   82 GERDRDRQRERRRDAKDREK--EKLKEKHREAEK-SHSRGKDREKEKDRRARK-EELRQT----VAHHNLLGQETRDRQL 153
Cdd:PTZ00121 1471 KADEAKKKAEEAKKADEAKKkaEEAKKKADEAKKaAEAKKKADEAKKAEEAKKaDEAKKAeeakKADEAKKAEEKKKADE 1550

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  154 LERAERKGRSVSKVRSEEKDEDSERGDEDRERRYRERKLQygdSKDNPLKYWLYKEEgerRHRKPREPDRDNKHREKSST 233
Cdd:PTZ00121 1551 LKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAE---EARIEEVMKLYEEE---KKMKAEEAKKAEEAKIKAEE 1624

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  234 REKREKySKEKSNSFSDKGEErhkEKRHKEGFHFDDERHQSNVDRKEKSAKDEPRKRES---QNGEHRNRGASSKRDGTS 310
Cdd:PTZ00121 1625 LKKAEE-EKKKVEQLKKKEAE---EKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEakkAEEDEKKAAEALKKEAEE 1700

                         330
                  ....*....|....*
gi 155030242  311 SQHAENLVRNHGKDK 325
Cdd:PTZ00121 1701 AKKAEELKKKEAEEK 1715
PTZ00121 PTZ00121
MAEBL; Provisional
 8-449 6.41e-07

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 53.99  E-value: 6.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    8 TKDDTWKADDLRKhlwaIQSGGSKEERKHREKKLRKESEMDLPEHKEPrcrdpdQDARsrdRVAEVHTAKESPRGERDRD 87
Cdd:PTZ00121 1093 TEEAFGKAEEAKK----TETGKAEEARKAEEAKKKAEDARKAEEARKA------EDAR---KAEEARKAEDAKRVEIARK 1159

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   88 RQRERR-RDAKDREKEKLKEKHREAEKSHSRGKDREKEKDRRArkEELRQTvahhnllgQETRDRQLLERAE--RKGRSV 164
Cdd:PTZ00121 1160 AEDARKaEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKA--EAARKA--------EEERKAEEARKAEdaKKAEAV 1229

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  165 SKVRSEEKDEDSERGDEDRERRYRERKLQYGDSKDNPLKYWLYKEEgerrhrKPREPDRDNKHREKSSTREKREKYSKEK 244
Cdd:PTZ00121 1230 KKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAE------EARKADELKKAEEKKKADEAKKAEEKKK 1303

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  245 SNSFSDKGEERHKEKRHKEgfhfDDERHQSNVDRKEKSAKDEPRKRESQNGEHRNRGASSKRDGTSSQHAENLVRNHGKD 324
Cdd:PTZ00121 1304 ADEAKKKAEEAKKADEAKK----KAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKK 1379

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  325 KDSRRKHGHEEGSSVwwKLDQRPGGEETVEIEKEETDLENARADAYTASCEDDFEDyeddfevcdgddDESSNEPESREK 404
Cdd:PTZ00121 1380 ADAAKKKAEEKKKAD--EAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKA------------DEAKKKAEEAKK 1445

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|
gi 155030242  405 LEELplaqKKEIQEIQRAINA-----ENERIGELSLKLFQKRGRTEFEKE 449
Cdd:PTZ00121 1446 ADEA----KKKAEEAKKAEEAkkkaeEAKKADEAKKKAEEAKKADEAKKK 1491
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 18-300 4.84e-06

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 50.89  E-value: 4.84e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    18 LRKHLWAIQSGGSKEERKHREKKLRKESEMdLPEHKEPRCRDPDQdarsRDRVAEVHTAKESprgerdrdrqRERRRDAK 97
Cdd:pfam17380  271 LNQLLHIVQHQKAVSERQQQEKFEKMEQER-LRQEKEEKAREVER----RRKLEEAEKARQA----------EMDRQAAI 335

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    98 DREKEKLK-EKHREAEKSHSRGKDREKEkdrRARKEELRQTVAHHNLLGQETRDRQLL-ERAERKGRSVSKVRSEEkdED 175
Cdd:pfam17380  336 YAEQERMAmERERELERIRQEERKRELE---RIRQEEIAMEISRMRELERLQMERQQKnERVRQELEAARKVKILE--EE 410

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   176 SERGDEDRERRYRERKLQYGDSKDNPLKYW----------LYKEEGERRHRKPR----EPDRDNKHREKSSTREKREKYS 241
Cdd:pfam17380  411 RQRKIQQQKVEMEQIRAEQEEARQREVRRLeeeraremerVRLEEQERQQQVERlrqqEEERKRKKLELEKEKRDRKRAE 490

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 155030242   242 KEKSNSFSDKGEERHK----EKRHKEGFHFDDERHQSNVDRKEKSAKDEPRKRESQNGEHRNR 300
Cdd:pfam17380  491 EQRRKILEKELEERKQamieEERKRKLLEKEMEERQKAIYEEERRREAEEERRKQQEMEERRR 553
PTZ00121 PTZ00121
MAEBL; Provisional
 1-294 5.17e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.83  E-value: 5.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    1 MEPGKRRTKDDTWKADDLRKHLWAIQSGGSKEERKHREKKLRKESEMDLPEHKEPRCRDPDQDARSRDRVAEVHTAKESP 80
Cdd:PTZ00121 1635 VEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEE 1714

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   81 RgerdrdrqrerrrdakdREKEKLKEKHREAEKSHSRGKDREKEKDRRArkEELRQTVAHHNLLGQETRDRQllERAERK 160
Cdd:PTZ00121 1715 K-----------------KKAEELKKAEEENKIKAEEAKKEAEEDKKKA--EEAKKDEEEKKKIAHLKKEEE--KKAEEI 1773

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  161 GRSVSKVRSEEKDEDSERGDEDRERRYRERK-----LQYGDSKDNPlkYWLYKEEGERRHRKpREPDRDNKHREKSSTRE 235
Cdd:PTZ00121 1774 RKEKEAVIEEELDEEDEKRRMEVDKKIKDIFdnfanIIEGGKEGNL--VINDSKEMEDSAIK-EVADSKNMQLEEADAFE 1850

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 155030242  236 KREKYSKEKSNSFSDKGEERHKEKRHKEgfhfDDERHQSNVDRKEKSAKDEPRKRESQN 294
Cdd:PTZ00121 1851 KHKFNKNNENGEDGNKEADFNKEKDLKE----DDEEEIEEADEIEKIDKDDIEREIPNN 1905
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 97-248 9.11e-05

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 46.42  E-value: 9.11e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    97 KDREKEKLKEKHREaekshsRGKDREKEKDRRARKEELRQTVAHHnllgqETRDRQLLERAERKGRSVSKVRSEEKDEDS 176
Cdd:TIGR01642    1 RDEEPDREREKSRG------RDRDRSSERPRRRSRDRSRFRDRHR-----RSRERSYREDSRPRDRRRYDSRSPRSLRYS 69

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 155030242   177 ERGDedrerryrerklqygdSKDNPlkywlykeegeRRHRKPREPDRDNKHREKSSTREKREKYSKEKSNSF 248
Cdd:TIGR01642   70 SVRR----------------SRDRP-----------RRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLW 114
PTZ00121 PTZ00121
MAEBL; Provisional
 2-307 3.07e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.13  E-value: 3.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    2 EPGKRRTKDDTWKADDLRKhlwaiqsggsKEERKHREKKLRKESEMdlpehKEPRCRDPDQDARSRDRVAEVHTAKESPR 81
Cdd:PTZ00121 1596 EVMKLYEEEKKMKAEEAKK----------AEEAKIKAEELKKAEEE-----KKKVEQLKKKEAEEKKKAEELKKAEEENK 1660

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   82 gerdrdrqRERRRDAKDREKEKLK-EKHREAEKSHSRGKDREKEKDRRARK-EELRQTVAhhnllgQETRDRQLLERAER 159
Cdd:PTZ00121 1661 --------IKAAEEAKKAEEDKKKaEEAKKAEEDEKKAAEALKKEAEEAKKaEELKKKEA------EEKKKAEELKKAEE 1726

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  160 KGRSVSKVRSEEKDEDSERGDEDRERRYRERKLQYgdskdnpLKYWLYKEEGERRHRKPR--EPDRDNKHREKSSTREKR 237
Cdd:PTZ00121 1727 ENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAH-------LKKEEEKKAEEIRKEKEAviEEELDEEDEKRRMEVDKK 1799

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 155030242  238 EKYSKEKSNSFSDKGEERH---KEKRHKEGFHFDDERHQSNVDRKE-KSAKDEPRKRESQNGEHRNRGASSKRD 307
Cdd:PTZ00121 1800 IKDIFDNFANIIEGGKEGNlviNDSKEMEDSAIKEVADSKNMQLEEaDAFEKHKFNKNNENGEDGNKEADFNKE 1873
PTZ00121 PTZ00121
MAEBL; Provisional
 2-317 4.19e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 44.75  E-value: 4.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    2 EPGKRRTKDDTWKADDLRKhlwaiqsggsKEERKHREKKLRKESEMDlpehkeprcrdpdqdarsRDRVAEVHTAKESPR 81
Cdd:PTZ00121 1367 EAAEKKKEEAKKKADAAKK----------KAEEKKKADEAKKKAEED------------------KKKADELKKAAAAKK 1418

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   82 GERDRDRQRERRRDA-----KDREKEKLKEKHREAEKshSRGKDREKEKDRRARKEELRQTVAHHNLLGQETRDRQllER 156
Cdd:PTZ00121 1419 KADEAKKKAEEKKKAdeakkKAEEAKKADEAKKKAEE--AKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKA--EE 1494

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  157 AERKGRSVSKVRSEEKDEDSERGDEDRERRYRERKLQYGDSKDNplkywLYKEEGERRHRKPREPDRDNKHREKSSTREK 236
Cdd:PTZ00121 1495 AKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADE-----AKKAEEKKKADELKKAEELKKAEEKKKAEEA 1569

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242  237 REkySKEKSNSFSDKGEERHK--EKRHKEGFHFDDERHQSNVD--RKEKSAKDEPRKRESQNGEHRNRGASSKRDGTSSQ 312
Cdd:PTZ00121 1570 KK--AEEDKNMALRKAEEAKKaeEARIEEVMKLYEEEKKMKAEeaKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKK 1647


                  ....*
gi 155030242  313 HAENL 317
Cdd:PTZ00121 1648 KAEEL 1652
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 217-306 4.34e-04

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 44.11  E-value: 4.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   217 KPREPDRDN-----KHREKSSTREKREKYSKEKSNSFSDKGEER--HKEKRHKEGFHFDDERHQSNVDRKEKSAKDEPRK 289
Cdd:TIGR01642    1 RDEEPDREReksrgRDRDRSSERPRRRSRDRSRFRDRHRRSRERsyREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRR 80

                           90       100
                   ....*....|....*....|
gi 155030242   290 RE---SQNGEHRNRGASSKR 306
Cdd:TIGR01642   81 RSrsvRSIEQHRRRLRDRSP 100
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 207-326 1.00e-03

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 42.98  E-value: 1.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   207 YKEEGERRHRKPREPDRDNKHREKSSTREKREKYSKEKSnsfSDKGEERHKEKrhkegfhfDDERhqsnvDRKEKSAKDE 286
Cdd:TIGR01622    2 YRDRERERLRDSSSAGDRDRRRDKGRERSRDRSRDRERS---RSRRRDRHRDR--------DYYR-----GRERRSRSRR 65

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 155030242   287 PRKRESQNGEHRNRGASSKRDGTSSQHAENLVRNHGKDKD 326
Cdd:TIGR01622   66 PNRRYRPREKRRRRGDSYRRRRDDRRSRREKPRARDGTPE 105
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 105-262 1.05e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 42.96  E-value: 1.05e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   105 KEKHREAEKSHSRGKDREKEKDRRARKEELRQtvahhnllgqETRDRQLLERAERKG-RSVSKVRSEEKDEDSERgdedr 183
Cdd:TIGR01642    3 EEPDREREKSRGRDRDRSSERPRRRSRDRSRF----------RDRHRRSRERSYREDsRPRDRRRYDSRSPRSLR----- 67

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 155030242   184 erryrerklqygdskdnplkywlykeegERRHRKPREPDRdnkHREKSSTREKREkysKEKSNSFSDKGEERHKEKRHK 262
Cdd:TIGR01642   68 ----------------------------YSSVRRSRDRPR---RRSRSVRSIEQH---RRRLRDRSPSNQWRKDDKKRS 112
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 912-984 1.21e-03

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 41.94  E-value: 1.21e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 155030242  912 VNVIDFSPFGEPiFLAGCSDGSIRLHQLSSAFPLLQWDSSTDshAVTGLQWSPTRpAVFLVQDDTSNIYIWDL 984
Cdd:cd00200   180 VNSVAFSPDGEK-LLSSSSDGTIKLWDLSTGKCLGTLRGHEN--GVNSVAFSPDG-YLLASGSEDGTIRVWDL 248
Caldesmon pfam02029
Caldesmon;
59-317 5.92e-03

Caldesmon;


Pssm-ID: 460421 [Multi-domain]  Cd Length: 495  Bit Score: 40.62  E-value: 5.92e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    59 DPDQDARSRDRVAevhtAKESPRGERDRDRQRERRRDAKDREKEKLKEKHREAEKSHSRGKDREKEKDRRARKEELRQTV 138
Cdd:pfam02029    3 DEEEAARERRRRA----REERRRQKEEEEPSGQVTESVEPNEHNSYEEDSELKPSGQGGLDEEEAFLDRTAKREERRQKR 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   139 AHHNLLGQETRDRQLLER----AERKGR----SVSKVRSEEKDEDSERGDEDRERRYRERKLQYGDSKDNPLKywlYKEE 210
Cdd:pfam02029   79 LQEALERQKEFDPTIADEkesvAERKENneeeENSSWEKEEKRDSRLGRYKEEETEIREKEYQENKWSTEVRQ---AEEE 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   211 GERRHRKPRE----PDRDNKHREKSSTREKREKYSKEKSNSFSDKGEERHKEK------RHKEGFHFDDERHQSNVDRKE 280
Cdd:pfam02029  156 GEEEEDKSEEaeevPTENFAKEEVKDEKIKKEKKVKYESKVFLDQKRGHPEVKsqngeeEVTKLKVTTKRRQGGLSQSQE 235

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 155030242   281 KSAKDEPRKRESQNGEHRNRgassKRDGTSSQHAENL 317
Cdd:pfam02029  236 REEEAEVFLEAEQKLEELRR----RRQEKESEEFEKL 268
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 2-238 7.39e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 40.27  E-value: 7.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242    2 EPGKRRTKDDTWKADDLRKHLWAIQSGGSKEERKHREKKLRKESEMDLPEHKEPRCRDPDQDARSRDRVAEVHTAKESPR 81
Cdd:PRK12678   74 AAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPA 153

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 155030242   82 GERDRDRQRERRRDAKDREKEklkEKHREAEKSHSRGKDREKEKDRRARKEELRQTVAHHNllGQETRDRQLLERAERKG 161
Cdd:PRK12678  154 TEARADAAERTEEEERDERRR---RGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQ--GDRREERGRRDGGDRRG 228

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 155030242  162 RSVSKVRSEEKDEDSERGDedrerryrerklQYGDSKDNplkywlyKEEGERRHRKPRepDRDNKHREKSSTREKRE 238
Cdd:PRK12678  229 RRRRRDRRDARGDDNREDR------------GDRDGDDG-------EGRGGRRGRRFR--DRDRRGRRGGDGGNERE 284
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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